Evolutionary Design of a DDPD Model of Ligation

  • Mark A. Bedau
  • Andrew Buchanan
  • Gianluca Gazzola
  • Martin Hanczyc
  • Thomas Maeke
  • John McCaskill
  • Irene Poli
  • Norman H. Packard
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3871)


Ligation is a form of chemical self-assembly that involves dynamic formation of strong covalent bonds in the presence of weak associative forces. We study an extremely simple form of ligation by means of a dissipative particle dynamics (DPD) model extended to include the dynamic making and breaking of strong bonds, which we term dynamically bonding dissipative particle dynamics (DDPD). Then we use a chemical genetic algorithm (CGA) to optimize the model’s parameters to achieve a limited form of ligation of trimers—a proof of principle for the evolutionary design of self-assembling chemical systems.


Strong Bond Chemical System Dissipative Particle Dynamic Random Force Evolutionary Design 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Mark A. Bedau
    • 1
    • 2
    • 3
  • Andrew Buchanan
    • 1
    • 2
  • Gianluca Gazzola
    • 1
    • 2
  • Martin Hanczyc
    • 1
    • 2
  • Thomas Maeke
    • 2
    • 4
  • John McCaskill
    • 2
    • 4
  • Irene Poli
    • 2
    • 5
  • Norman H. Packard
    • 1
    • 2
  1. 1.Protolife S.r.l.Marghera, VeneziaItaly
  2. 2.European Center for Living TechnologyVeneziaItaly
  3. 3.Reed CollegePortlandUSA
  4. 4.Biomolecular Information Processing, Ruhr-Universitat BochumSankt AugustinGermany
  5. 5.University of Venice Ca’ FoscariVeneziaItaly

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